Mycobacterium tuberculosis (M.tb) infects a new human host every second. It is not known why M.tb is such a successful pathogen, and it is unexpected given the current understanding of how M.tb evolves. The long-term goal of this research is to identify ecological and evolutionary processes driving emergence and maintenance of pathogenic traits in microbial populations. The objective of this proposal is to understand effects of recombination and variable TB transmission on evolution of M.tb. The central hypothesis is: apparently paradoxical features of M.tb evolution are due to the unrecognized influence of cryptic recombination and extreme variability of TB transmission. The rationale for the proposed research is the central role of recombination and reproductive dynamics in shaping patterns of genetic diversity. Two specific aims will be used to test this hypothesis: 1) Characterize lateral gene transfer (LGT) among pathogenic mycobacteria; and 2) Quantify TB transmission variability and measure its effects on M.tb evolution. In Aim 1, patterns of recombination will be inferred from high resolution genomic data in natural populations of mycobacteria; LGT will be further characterized in an experimental system. In Aim 2, genomic and epidemiological data from a well-characterized M.tb meta- population will be analyzed for signatures of variability in TB transmission. Best fit population genetic models will also be identified for M.tb populations, and parameters of these models compared with benchmark values inferred from epidemiological data. By tackling the unexplored paradox of TB's persistence as a threat to global health despite apparent limitations on M.tb adaptability, the proposed project offers an innovative alternative to current perspectives on M.tb evolution. This research will provide greater insight into how M.tb evolves, which is needed to understand why these populations are so resilient, and ultimately to design better strategies of controlling or even eradicating TB. It will also open new avenues of research to identify effects of cryptic re- combination and heterogeneous transmission on evolution of other bacterial pathogens.